Control over protein synthesis and degradation rates is involved in the regulation of most biological processes and is believed to be the primary cause of numerous diseases. Regulation of the synthesis rates of biomolecules in living systems is one of the most fundamental features of biochemical and physiologic control. For this reason, measurement of biosynthetic and degradation rates in vivo has been the subject of enormous research effort over the past 50 years. Among the macromolecules that have been studied, proteins have received perhaps the most intense attention due to their central role in controlling biological processes. The measurement of protein synthesis has traditionally required the use of isotopic labels (stable isotopes or radioisotopes).
Spatially controlled protein production and directed delivery of newly synthesized proteins are fundamental processes in the development, maintenance, and adaptation of specialized cellular structures. Local protein synthesis allows for the rapid production of proteins in regions of the cell where they are needed. For example, spatially localized protein translation is associated with myofibril growth in cardiac myocytes (Larsen and Saetersdal, 1998) and contributes to actin production at the leading edge of migrating fibroblasts (Huttelmaier et al., 2005; Rodriguez et al., 2006). In neurons, local protein production is especially important in establishing the complex architecture of the cell and in restricting activity-dependent changes to subsets of synapses. During neuronal development, guidance of axons to their targets involves the localized induction of translation in the axonal growth cone by extracellular factors (Leung et al., 2006; Wu et al., 2005). In mature neurons, distal dendrites locally synthesize proteins in response to neuronal pathway stimulation or local application of growth factors or neurotransmitters (Ouyang et al., 1999; Steward and Worley, 2002; Aakalu et al., 2001; Ju et al., 2004; Kacharmina et al., 2000; Muddashetty et al., 2007; Smith et al., 2005; Todd et al., 2003). The induction of long-term potentiation (LTP), an electrophysiological model of learning, induces the redistribution of polyribosomes to sites near synapses and the enlargement of a polyribosome-associated subset of synapses (Harris et al., 2003; Ostroff et al., 2002), and dendritic translation is required for LTP and learning (Bradshaw et al., 2003; Miller et al., 2003). These results suggest that activity-dependent local protein synthesis may contribute to synapse growth during learning. Interestingly, the Fragile X mental retardation protein FMRP is required for stimulus-induced translation of a subset of dendritic messages (Muddashetty et al., 2007), implying that abnormalities in activity-dependent local protein synthesis may underlie some disorders of mental cognition as well.
Delivery of newly synthesized proteins to subcellular regions by various protein trafficking mechanisms is also essential in maintaining specialized cellular functions. For example, protein sorting within the secretory pathway allows for long-distance transport of proteins from their site of synthesis at the endoplasmic reticulum to discrete final destinations within the cell. This process is necessary for the establishment and maintenance of polarized epithelial cells and of axonal and dendritic specializations in neurons, including pre- and postsynaptic complexes (Horton and Ehlers, 2003; Horton et al., 2005; Muth and Caplan, 2003). Aside from the well studied processes of protein trafficking and local protein translation, protein delivery to specific subsets of structures in cells could conceivably occur due to spatially localized demands for particular proteins. For example, in neurons, synapses undergoing potentiation or growth can be expected to accumulate recently synthesized structural proteins at higher rates than stable synapses. Incorporation of molecules from regional pools of recently synthesized proteins by specific synapses would represent a step in protein delivery distinct from protein trafficking or activity-dependent local protein synthesis. In the case of proteins that arrive in dendrites by trafficking or local synthesis, accumulation in specific “receptive” synapses could represent a subsequent final step in spatially regulated protein delivery.